Errors from `compute_pairwise_resnik`

[caufieldjh]

Hello!

We're trying to put together some unit tests for computing pairwise Resnik similarity, but are encountering an error with a description that doesn't seem correct.

With the input here and a test like this:

    def setUp(self) -> None:
        """Set up."""
        self.test_graph_path_nodes = "tests/resources/test_hpo_nodes.tsv"
        self.test_graph_path_edges = "tests/resources/test_hpo_edges.tsv"
        self.resnik_outpath = "tests/output/resnik_out"
        self.test_graph = Graph.from_csv(
            directed=True,
            node_path=self.test_graph_path_nodes,
            edge_path=self.test_graph_path_edges,
            nodes_column="id",
            node_list_node_types_column="category",
            sources_column="subject",
            destinations_column="object",
            edge_list_edge_types_column="predicate",
        )
        self.test_counts = {
            "HP:0000118": 23,
            "HP:0000001": 24,
            "HP:0001507": 1,
            "HP:0001574": 1,
            "HP:0001871": 1,
            "HP:0033127": 1,
            "HP:0025354": 1,
            "HP:0001608": 1,
            "HP:0001197": 1,
            "HP:0000119": 1,
            "HP:0001939": 1,
            "HP:0000707": 1,
            "HP:0025031": 1,
            "HP:0001626": 1,
            "HP:0000818": 1,
            "HP:0025142": 1,
            "HP:0002086": 1,
            "HP:0002715": 1,
            "HP:0000478": 1,
            "HP:0040064": 1,
            "HP:0002664": 1,
            "HP:0000598": 1,
            "HP:0000769": 1,
            "HP:0045027": 1,
            "HP:0000152": 1,
        }

...

    def test_compute_pairwise_resnik(self) -> None:
        """Test pairwise Resnik computation."""

        compute_pairwise_resnik(
            dag=self.test_graph,
            counts=self.test_counts,
            path=self.resnik_outpath,
        )
        self.assertTrue(os.path.exists(self.resnik_outpath))

we consistently get an error like this:

ValueError: The provided two nodes 3 and 1 do not have a shared parent node. Perhaps, the provided DAG has multiple root nodes and these two nodes are in different root portions of the DAG. Another analogous explanation is that the two nodes may be in different connected components.

Any idea what's going on here? The two nodes definitely have shared ancestry and are in the same DAG. Does this have something to do with the directionality of the graph? A full version of HPO subclass_of nodes/edges works without issue.

@hrshdhgd @justaddcoffee

[LucaCappelletti94]

Solved in a brief call, the issue was that the graph was transposed, i.e. the root node was a leaf as the edge list described. We used the to_transposed method to convert it to the desired shape.